Contact Information

Name
Kota KASAHARA, Ph.D.
Position
Assistant Professor
Affiliation
Computational Structural Biology Lab., College of Life Sciences, Ritsumeikan University, Japan
Address
1-1-1, Noji-higashi, Kusatsu-shi, Shiga, 525-8577, Japan
E-mail
ktkshr <at> fc.ritsumeikan.ac.jp

Publication List

Articles

  • *: Corresponding author(s). / †: Joint first authors.
    1. †Naoki Ogasawara​, *†Kota Kasahara​​, Ryosuke Iwai, Takuya Takahashi,
      Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations,
      2018, PeerJ, 6:e4769, doi: 10.7717/peerj.4769, URL
    2. *Kota Kasahara, Shun Sakuraba, Ikuo Fukuda,
      Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation,
      2018, The Journal of Physical Chemistry B, 122(9):2495-2503, doi: 10.1021/acs.jpcb.7b10830, PubMed URL
    3. Tomonori Hayami Kota Kasahara Haruki Nakamura *Junichi Higo,
      Molecular Dynamics Coupled with a Virtual System for Effective Conformational Sampling,
      2018, Journal of Computational Chemistry, , doi: 10.1002/jcc.25196, PubMed URL
    4. *†Kota Kasahara, *†Masaaki Shiina, Junichi Higo, Kazuhiro Ogata, Haruki Nakamura,
      Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.,
      2018, Nucleic Acids Research, 46(5):2243-2251, doi: 10.1093/nar/gkx1297, PubMed URL
    5. *Junichi Higo, Kota Kasahara, BHaruki Nakamura,
      Multi-dimensional virtual system introduced to enhance canonical sampling.,
      2017, The Journal of Chemical Physics, 147: 134102, doi: 10.1063/1.4986129, PubMed URL
    6. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation.,
      2017, Information Engineering Express, 3(2): 11-23, , URL
    7. *Kasahara K, Shiina M, Fukuda I, Ogata K, Nakamura H,
      Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer.,
      2017, PLoS ONE, 12(2): e0172654, doi:10.1371/journal.pone.0172654, URL
    8. *Junichi Higo, Kota Kasahara, Bhaskar Dasgupta, Haruki Nakamura,
      Enhancement of canonical sampling by virtual-state transitions,
      2017, The Journal of Chemical Physics, 146(044104):1-12, doi: 10.1063/1.4974087, PubMed URL
    9. Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara,
      An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL,
      2017, International Journal of Networked and Distributed Computing, 5(1):52-61, doi: 10.1109/ICIS.2016.7550743, URL
    10. Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      IBiSA_tools: A Computational Toolkit for Ion-binding State Analysis in Molecular Dynamics Trajectories of Ion Channels ,
      2016, PLoS ONE, 11(12): e0167524, doi: 10.1371/journal.pone.0167524, PubMed URL
    11. Kota Kasahara, Benson Ma, Kota Goto, Bhaskar Dasgupta, Junichi Higo, Ikuo Fukuda, Tadaaki Mashimo, Yutaka Akiyama, Haruki Nakamura,
      myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme,
      2016, Biophysics and Physicobiology, 13:209-216, doi: 10.2142/biophysico.13.0_209, PubMed URL
    12. Kota Kasahara, *Kengo Kinoshita,
      Landscape of protein-small ligand binding modes.,
      2016, Protein Sci, 25(9):1659-71, doi: 10.1002/pro.2971, PubMed URL
    13. Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories,
      2016, Bioinformatics, 32(16):2531-3, doi: 10.1093/bioinformatics/btw129, PubMed URL
    14. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction,
      2016, PLoS ONE, 11:e0150716, doi: 10.1371/journal.pone.0150716, PubMed URL
    15. *Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi, Haruki Nakamura,
      Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.,
      2015, J Comput Chem, 36(20):1489-501, doi: 10.1002/jcc.23948, PubMed URL
    16. Kota Kasahara, Ikuo Fukuda, Haruki Nakamura,
      A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer-DNA Complex.,
      2014, PLoS ONE, 9:e112419, doi: 10.1371/journal.pone.0112419, PubMed URL
    17. Bhaskar Dasgupta, Kota Kasahara, Narutoshi Kamiya, Haruki Nakamura, *Akira R Kinjo,
      Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics,
      2014, PLoS ONE, 9:e91347, doi: 10.1371/journal.pone.0091347, PubMed URL
    18. Kota Kasahara, *Kengo Kinoshita,
      GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes.,
      2014, BMC Bioinformatics, 15:12, doi: 10.1186/1471-2105-15-12, PubMed URL
    19. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      Ion Concentration-Dependent Ion Conduction Mechanism of a Voltage-Sensitive Potassium Channel.,
      2013, PLoS ONE, 8:e56342, doi: 10.1371/journal.pone.0056342, PubMed URL
    20. Kota Kasahara, Matsuyuki Shirota, *Kengo Kinoshita,
      Comprehensive classification and diversity assessment of atomic contacts in protein-small ligand interactions.,
      2013, J Chem Inf Model, 53:241–248, doi: 10.1021/ci300377f, PubMed URL
    21. *Takeshi Obayashi, Kozo Nishida, Kota Kasahara, Kengo Kinoshita,
      ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.,
      2011, Plant Cell Physiol, 52:213–219, doi: 10.1093/pcp/pcq203, PubMed URL
    22. *Kota Kasahara, Kengo KinoshitK, Toshihisa Takagi,
      Ligand-binding site prediction of proteins based on known fragment-fragment interactions.,
      2010, Bioinformatics, 26:1493–1499, doi: 10.1093/bioinformatics/btq232, PubMed URL
    23. Kota Kasahara, Hideyuki Tsuboi, Michihisa Koyama, Akira Endou, Momoji Kubo, Calros Adriel Del Carpio, *Akira Miyamoto,
      Tight-Binding Quantum Chemical Molecular Dynamics Study on First Proton Transfer Process of ORR Catalyzed by Cobalt-Porphyrin Complex.,
      2006, Electrochem Solid-State Lett, 9:A490, doi: 10.1149/1.2336985, URL

    Reviews (Japanese)

    1. Kasahara K, Shirota M, Kinoshita K Molecular dynamics simulation, ion channel, dynamic structure, bioinformatics 2013 Seikagaku 85(8):656-662 PubMed

    Books (Japanese)

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    Software/Database

    Curriculum Vitae

    C.V.

    Jan 8th, 1983
    Hello, world.
    Apr,1st,1998−Mar,19th,2003
    Department of Material Engeneering, Nagaoka College, National Institute of Technology, Japan
    Apr,1st,2003−Mar,2005
    Department of Applied Chemistry, School of Engeneering, Tohoku University
    Undergraduate student
    (Supervisor: Prof. Akira Miyamoto)
    Apr,1st,2005−Mar,27th,2007
    Department of Applied Chemistry, Graduate School of Engeneering, Tohoku University
    Master course student
    (Supervisor: Prof. Akira Miyamoto)
    Apr,1st,2007−Sep,27th,2010
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo
    Ph.D. course student
    (Supervisor: Prof. Toshihisa Takagi)
    Apr,2008−Mar,2009
    Research Fellow of the Japan Society for the Promotion of Science (DC2)
    Oct,1st,2010−Dec,31st,2012
    Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University
    Postdoc.
    (PI: Prof. Kengo Kinoshita)
    Jan,1st,2013−Mar,31st,2016
    Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University
    Postdoc.
    (PI: Prof. Haruki Nakamura)
    Apr,1st,2016−Present
    Department of Bioinformatics, College of Life Sciences, Ritsumeikan University
    Assistant Professor.
    (PI: Prof. Takuya Takahashi)

    Affiliated Academic Organizations

    • Protein Science Society of Japan
    • Biophisical Society of Japan
    • Japanese Society for Bioinformatics